Surface Charge Density Profile Research Articles

Message-passing neural network based multi-task deep-learning framework for COSMO-SAC based σ-profile and VCOSMO prediction

• A message-passing neural network based feedforward neural network (MPNN-FNN) is developed for σ-profile and V COSMO prediction. • Hybrid molecular representations are utilized to extract the molecular features. • The proposed model can well discriminate the cis/trans and structural isomers. • The IDAC calculated by predicted σ -profile and V COSMO is very close to the QM derived ones. The correct implementation of the quantum mechanics (QM) calculation for COSMO-SAC based surface charge density profiles ( σ -profile) and cavity volumes ( V COSMO ) is tricky and time-consuming. As a shortcut, the GC approaches (GC-COSMO) were proposed to predict the required σ -profile and V COSMO for COSMO based methods. However, the GC-COSMO model cannot discriminate the isomers and cannot predict the complex molecules due to a lack of diverse functional groups. In this context, a message-passing neural network based feedforward neural network (MPNN-FNN) is proposed for rapid and accurate predicting COSMO-SAC based σ -profile and V COSMO . The hybrid molecular representation integrated the message-passing neural network (MPNN) learned representations and 200 additional molecule-level RDKit features, which can capture both local and global features of the overall molecule, is utilized to develop a better molecular feature extraction model. Based on the hybrid molecular representations, a feedforward neural network (FNN) model for the σ -profile and V COSMO prediction is trained and tested on the VT-2005 database. The developed MPNN-FNN model demonstrates significantly better performance than the GC-COSMO method and can well discriminate the cis/trans and structural isomers. In addition, the calculation speed based on the proposed model for COSMO-SAC based infinite dilution activity coefficient (IDAC) reaches about 100 compounds per second, which are the prerequisite to performing a high throughput green solvent screening.

Transformer-convolutional neural network for surface charge density profile prediction: Enabling high-throughput solvent screening with COSMO-SAC

A deep learning (DL) method for quickly predicting surface charge density profiles (σ-profile) and cavity volumes (VCOSMO) of molecules for the COSMO-SAC model is developed. The molecular fingerprints are derived from the encoder state of a Transformer model pre-trained on the ChEMBL database, which allows transfer learning from large-scale unlabeled data and improve generalization performance by developing better molecular fingerprints for building models with significantly smaller datasets. Employing the pre-trained molecular fingerprints, a convolutional neural network (CNN) model for the σ-profile and VCOSMO prediction is trained and tested on the VT-2005 database. The obtained Transformer-CNN model presents superior performance to the GC-COSMO approach and enables the prediction of σ-profile and VCOSMO of millions of molecules in only a few minutes. Taking advantages of the model, a high-throughput solvent screening framework based on COSMO-SAC is further proposed and exemplified by searching sustainable solvent for the deterpenation process of citrus essential oils.

Odor prediction and aroma mixture design using machine learning model and molecular surface charge density profiles

Structure-Odor Relationship (SOR) is the key to the understanding of the mechanism of odors, which further facilitates the odor prediction and aroma design. However, the modeling of SOR is still a challenge since the understanding of odor mechanism is unresolved. In this paper, an Artificial Neural Network (ANN) model is developed to generate the SOR model for aroma mixtures, in which the molecular surface charge density profiles (σ-profiles) are used as the descriptors. In this ANN model, the aroma mixture properties are the input, and the σ-profiles of the mixtures are the output, which can directly predict the σ-profiles of the aroma mixtures under certain odor requirements. Then, Euclidean distance-based ingredient screening method is applied to search the aroma mixture that fits the predicted σ-profiles from the ANN model. Finally, a Computer-Aided Aroma Design (CAAD) framework is formulated for the design of aroma mixtures. Two case studies of aroma mixture design are presented. The results are verified by the electronic nose, which highlight the effect of the developed SOR model as well as the CAAD framework.

Machine learning‐based atom contribution method for the prediction of surface charge density profiles and solvent design

AbstractSolvents are widely used in chemical processes. The use of efficient model‐based solvent selection techniques is an option worth considering for rapid identification of candidates with better economic, environment and human health properties. In this paper, an optimization‐based MLAC‐CAMD framework is established for solvent design, where a novel machine learning‐based atom contribution method is developed to predict molecular surface charge density profiles (σ‐profiles). In this method, weighted atom‐centered symmetry functions are associated with atomic σ‐profiles using a high‐dimensional neural network model, successfully leading to a higher prediction accuracy in molecular σ‐profiles and better isomer identifications compared with group contribution methods. The new method is integrated with the computer‐aided molecular design technique by formulating and solving a mixed‐integer nonlinear programming model, where model complexities are managed with a decomposition‐based strategy. Finally, two case studies involving crystallization and reaction are presented to highlight the wide applicability and effectiveness of the MLAC‐CAMD framework.

A universal cohesive energy estimation equation based on COSMO

AbstractA universal cohesive energy estimation equation for neutral molecules based on COSMO (COSMO‐UCE) was developed in this work; which comprises contributions from dispersive (nonpolar), polar (electrostatic) and hydrogen‐bonding interactions, and takes into account the influence of local segment surface charge density profile and entire molecule stereo charge distribution (dipole and quadrupole moment) on coulombic and hydrogen‐bonding interaction energy calculations. We have examined this model for the molar cohesive energy of pure liquids, gases, and ionic liquids (ILs) with successful results, which indicates that this model is reliable for calculating the molar cohesive energy of conventional fluids (nonpolar, polar, and hydrogen‐bonding liquids and gases) and ILs. This model can be used for solubility parameter calculations and solvent selections for chemical separation process (gas absorption and liquid–liquid extraction).

COSMO-descriptor based computer-aided ionic liquid design for separation processes. Part I: Modified group contribution methodology for predicting surface charge density profile of ionic liquids

When applying COSMO-based models in Computer-Aided Ionic Liquid Design (CAILD), the generation of surface charge density profiles (σ-profiles) and cavity volumes (VCOSMO) of ILs is particularly important but too computationally expensive with quantum chemical calculations. In this work, a modified group contribution methodology, the COSMO-GC-IL method, is proposed for quick prediction of IL σ-profiles and VCOSMO based on σ-profiles of IL groups in their reference states (COSMO descriptors), together with two modification parameters (stretch and translation parameters). The influence of molecular environment on target groups can be well described and IL isomers are thereby distinguishable. To verify the method, σ-profiles and VCOSMO generated from the present method and from the DMol3 database are employed to calculate activity coefficients of 28,644 binary systems and 3410 liquid-liquid equilibria of ternary mixtures. Their close results in most cases demonstrate the reliability of the COSMO-GC-IL method.

DC flashover characteristics of a polymeric insulator in presence of surface charges

Effect of surface charges on dc flashover characteristics of a composite polymeric insulator is studied by means of experiments and theoretical calculations. The considered insulator consisted of a glass fiber reinforced epoxy core covered with a layer of silicone rubber and terminated by metallic electrodes with rounded smooth edges. In the experiments, the insulator surface was charged by external corona while keeping the electrodes grounded and different charging levels were realized by varying its intensity. A series of disruptive discharge tests were carried out on the charged insulator under negative dc voltages. It was revealed that negative deposited surface charges led to an enhancement of the flashover performance whereas positive ones reduced the flashover voltage level. A theoretical model has been developed and utilized for analyzing the experimental results. In the model, surface charge density profiles deduced from measured surface potential distributions were used as boundary conditions for calculations of electric fields. The measured and calculated flashover voltages were found to be in agreement indicating that the observed variations in the flashover characteristics could be attributed to the modifications of the electric field produced by the surface charges.

Additional considerations about the role of ion size in charge reversal

The effect of the ion size on the charge reversal process is studied via canonicalMonte Carlo simulation. To this end, a primitive model of electrolyte is usedto analyze the electric double layer formed by an asymmetric electrolyte in thepresence of a charged planar wall. Different values of ion diameters and surfacecharge densities are used so as to determine the conditions at which the chargereversal first occurs. For each case, the apparent surface charge density is calculatedas a function of the distance from the charged wall for the different electrolyteconcentrations in order to establish the minimal salt concentration required for the chargereversal. We will refer to this electrolyte concentration as the reversal concentrationand will show how it depends on the surface charge density and on the ion size.From the apparent surface charge density profiles, the distance from the wallat which the charge reversal arises as well as its intensity can be also inferred.

Restoring Charge Asymmetry in Continuum Electrostatics Calculations of Hydration Free Energies

Implicit solvation models are symmetric with respect to charge inversion. On the other hand, explicit solvent simulations show significant asymmetry in hydration free energies with respect to charge reversal. It has not been obvious how implicit solvation models can be modified in a general way to address this serious shortcoming. We solve this problem by using the induced surface charge density (ISCD) obtained from a boundary element solution of the Poisson equation to derive a simple customized correction for the Born radius of each atom. This simple correction restores the charge asymmetry and reproduces the hydration free energies from free energy perturbation calculations with a high degree of fidelity. The induced surface charge density profile of an atom essentially provides a measure of the average preferred orientation of a water molecule in the first solvation shell, thereby allowing a proper assignment of the dielectric boundary. We refer to these modified radii as ISCD-corrected Born radii.

Prediction of Partition Coefficients of Benzothiophene and Benzothiophene 1,1-Dioxide in Octane/Acetonitrile System Using COSMO Theory

The partition coefficients of benzothiophene (BT) and benzothiophene 1,1-dioxide (BTDO) in the octane/acetonitrile system were predicted using the COSMO (conductor-like screening model) based activity coefficient models COSMO-SAC (segment activity coefficient) and COSMO-UNIQUAC. In COSMO-UNIQUAC, a segment activity coefficient was described in a UNIQUAC-type equation. The results with COSMO-UNIQUAC were compared with those from the COSMO-SAC model. It was found that COSMO-UNIQUAC reproduced the experimental data more accurately than COSMO-SAC. The surface charge density profiles (σ-profiles) of functional groups on BT and BTDO molecules were utilized to determine that the partition coefficients of BTDO are much lower than those of BT. A hypothetical molecule with the volume and surface area of BTDO was conducted by using the σ-profiles of functional groups on BT and BTDO. The partition coefficients of the hypothetical component were predicted by COSMO-UNIQUAC. It was revealed that the partitions of BTDO i...

Group contribution prediction of surface charge density profiles for COSMO‐RS(Ol)

AbstractA new method for predicting the surface charge density distribution (σ profile) and cavity volume of molecules based on group contributions was developed. The original σ profiles used for the regression were obtained using Gaussian 03 B3LYP/6‐311G(d,p). In total 1363 σ profiles were used for the regression of group parameters. Group definitions are identical to those used previously for boiling point estimation. Original and estimated σ profiles were used to predict activity coefficients at infinite dilution and VLE data of binary systems using the COSMO‐RS(Ol) model. The results were compared with the experimental data stored in the Dortmund Data Bank. In many cases the results were of comparable accuracy. However, for a few compounds, poor results were obtained, in particular for conjugated components like nitrobenzenes. The method offers a fast and reliable generation of σ profiles to be used with COSMO‐RS(Ol) within its range of applicability. © 2007 American Institute of Chemical Engineers AIChE J, 2007

Vibrational modes of thin oblate clouds of charge

A numerical method is presented for finding the eigenfunctions (normal modes) and mode frequencies of azimuthally symmetric non-neutral plasmas confined in a Penning trap whose axial thickness is much smaller than their radial size. The plasma may be approximated as a charged disk in this limit; the normal modes and frequencies can be found if the surface charge density profile σ(r) of the disk and the trap bounce frequency profile ωz(r) are known. The dependence of the eigenfunctions and equilibrium plasma shapes on nonideal components of the confining Penning trap fields is discussed. The results of the calculation are compared with the experimental data of Weimer et al. [Phys. Rev. A 49, 3842 (1994)] and it is shown that the plasma in this experiment was probably hollow and had mode displacement functions that were concentrated near the center of the plasma.

Noncontact surface charge density profiles measurement on top and bottom of a charged film

Equivalent surface charge density profiles on both the top and bottom surfaces of corona-charged films were measured without any contact by using a surface potential voltmeter with a horizontal resolution of about 2 mm and a laser displacement meter with a vertical resolution of 10 mu m. A personal computer controls the sample position with a resolution of a few micrometers, which depends on a digital X-Y stage and a backside ground electrode position (distance from the bottom of the charged film). Surface potential profiles at a few different distances between the ground electrode (back) and the sample film were recorded on a floppy disk, and equivalent surface charge density profiles on the top and the bottom of the film were calculated and plotted automatically by using a personal computer. Some interesting electrostatic phenomena related to their charge behavior are reported as are its applications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>

The interpretation of experimentally derived helium-metal interaction potentials

We show that existing theories which relate the helium-metal potential to the metallic surface charge density do not lead to a unique prediction for the surface charge density profile for a given experimental potential. A simple calculation of the corrugation of the attractive van der Waals potential for Cu(110) and Ag(110) shows that this is a contributary factor and that its inclusion improves the agreement between theories and also between experimental and calculated values for the charge density corrugation amplitude.

The interpretation of experimentally derived helium-metal interaction potentials

We show that existing theories which relate the helium-metal potential to the metallic surface charge density do not lead to a unique prediction for the surface charge density profile for a given experimental potential. A simple calculation of the corrugation of the attractive van der Waals potential for Cu(110) and Ag(110) shows that this is a contributary factor and that its inclusion improves the agreement between theories and also between experimental and calculated values for the charge density corrugation amplitude.

Theory of the surface dipole layer and of surface tension in liquids of charged particles

The problem of the surface density profiles and of the surface tension of a two-component liquid of charged particles in equilibrium with its vapour is examined. The exact equilibrium conditions for the profiles are given in terms of the inverse response functions of the inhomogeneous fluid and alternative exact expressions for the surface tension are derived. The use of a density gradient expansion reduces the problem to the knowledge of properties of a homogeneous charged fluid on a uniform neutralizing background, in which the total particle density and the charge density are independent variables. Additional simplifications are discussed for special cases for which a perturbative treatment of the surface charge density profile can be developed and, in particular, for nearly symmetric ionic liquids and for simple liquid metals.